RetrogeneDB ID: retro_chof_1069

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_192961:2707..3182(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RFFL
• Ensembl ID: ENSCHOG00000001950
• Aliases: None
• Description: ring finger and FYVE-like domain containing E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:24821]

Sequence

>retro_chof_1069
ACCCAGCCTCACACCAGCACAGCACCTCCTACCTCACCCAACCTCCGTTCTTCACCTACACAAGCCACCTTTGTTGGCCC
AGCTGGGACTCAGAAAAATCAGTAGGCCAATGGCTATGTGTCTCCAGACCAAGAGGAACCTGTCTACCTGGAGAGCACAG
CCAGAGTACCTGACTCAGGATGAGATCCAGTCCATTGACTCAGAGGATAGCTTTGTGCCAGGCCAGAGGGCTTCTCTGCC
TGACCTGACCAATCTGGAAGACATTGAAGCGCTGATTGTGTGGCAGCTGAAAGAGATCCTGGCCCACAACTTTGTCAGTT
ACAAGGGCTGCTGTGAGAAGTGGGAGCTGATGGAGAGGGTGCCTTGGCTGTACAAAGATCAAAAAGGACTCCAGCATCTG
GTTTGTGGTGCTGAAGATCAAAATGGGGGAGCGGTGCCACCTGGCATGGAGGAGAACCTATGTAATATCTTGTTG

Alignment

ORF - retro_chof_1069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.65 %
• Parental protein coverage: 52.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TQPHTSTAPSTSSNLPSSPTQATSVGPAQAQENQQANGHVSQDQEEPVYLESTARVP-AEDETQSIDSED
          TQPHTSTAP.TS.NL.SSPTQAT.VGPA..Q.NQ.ANG.VS.DQEEPVYLESTARVP...DE.QSIDSED
Retrocopy TQPHTSTAPPTSPNLRSSPTQATFVGPAGTQKNQ*ANGYVSPDQEEPVYLESTARVP>TQDEIQSIDSED

Parental  SFVPGRRASLSDLTNLEDIEALTVRQLKEILARNFVNYKGCCEKWELMERVTRLYKDQKGLQHLVCGAED
          SFVPG.RASL.DLTNLEDIEAL.V.QLKEILA.NFV.YKGCCEKWELMERV..LYKDQKGLQHLVCGAED
Retrocopy SFVPGQRASLPDLTNLEDIEALIVWQLKEILAHNFVSYKGCCEKWELMERVPWLYKDQKGLQHLVCGAED

Parental  QNGGAVPPSMEENLCKICM
          QNGGAVPP.MEENLC.I..
Retrocopy QNGGAVPPGMEENLCNILL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1069 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001950	2 retrocopies	retro_chof_1069 , retro_chof_285,
Macropus eugenii	ENSMEUG00000012628	1 retrocopy	retro_meug_1745,
Otolemur garnettii	ENSOGAG00000024777	1 retrocopy	retro_ogar_621,
Ochotona princeps	ENSOPRG00000011769	1 retrocopy	retro_opri_385,
Tarsius syrichta	ENSTSYG00000008923	2 retrocopies	retro_tsyr_1749, retro_tsyr_2060,